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Formation of heterologous (calf thymus double-stranded DNA) and homologous (linearized pBR322 plasmid double-stranded DNA) quadruplexes upon binding with the simple aliphatic tripeptide derivative (dansyl hydrazide trivaline) was examined by fluorimetry, flow linear and circular dichroism and electron microscopy. The morphology of the rod-like compact particles formed due to the association of double-stranded DNA segments proved to be the same for both DNAs, whereas the stability of the compact DNA structure upon tripeptide removal from the complex with DNA differed substantially for homologous versus non-homologous double-stranded DNA used. The increase of NaCl concentration in the solution up to 30 mM removes the peptide from both types of the complexes completely. At the same time at 20 mM NaCl calf thymus DNA quadruplexes readily dissociate, whereas the structures formed by plasmid DNA retain their morphology in the solution containing NaCl with concentrations up to 40 mM and are only partially disrupted at even higher NaCl concentration. These results provide the analogy between trivaline-DNA model complexes and RecA-DNA binding.

The protein-free method was applied for the investigation of histone H1 DNA complexes formation. The main advantage of this method is the possibility to get intramolecular compact structures at interaction of individual spread molecules of DNA with histone H1. It was shown that in the presence of 0.2-5 micrograms/ml of histone H1 in hypophase there are three types of structures on electronmicroscopic preparations: fibres of non-compacted DNA, compact fibres with twisted strands of duplex DNA and compacted rod-like and circular structures where separate fibres of duplex DNA could not be distinguished. The study of compact structures morphology allows to conclude that they are formed by side-by-side association of DNA fibres, as it takes place in the case of triple rings formation at the compactization of circular DNA due to trivaline binding. At increasing ionic strength there is a tendency for transition from second type structures to the third type structures. The latter can be explained by transition from non-cooperative to cooperative binding of histone H1 to DNA.

The cytoskeleton is considered to be a very important cellular component, playing a role in the interactions between different organelles. However, in many cases the true biochemical functions and some of the structural aspects of cytoskeletal filaments are still unknown. Several hybridoma cell lines producing monoclonal antibodies (Mab) against a complex of linear DNA with the tridecapeptide Dns-NH2-VVTGVKTGVKTVT-CO2H have been established. (Dns is 5-methylaminonaphthalene-1-sulphonic acid.) The organization of this complex, in which the DNA is in a compact form, has been well-characterized previously by physicochemical methods and electron microscopy. A monoclonal antibody, Mab 66/9, was selected for further study on the basis of its reactivity with the immunizing DNA-peptide complex and minimal reaction with DNA alone. In immunofluorescence studies with cultured cells, this Mab did not recognize any nuclear structures, but reacted with cytoskeletal intermediate filaments and with nuclear lamins. Thus, Mab 66/9 appears to define an epitope present in the immunizing DNA-peptide complex and in cytoskeletal elements. The epitope is probably determined by the conformation of the oligopeptide since it was not detected in denatured cell lysates. Our observations provide some indirect evidence in support of the DNA-binding properties of cytoskeletal components which have been hypothesized in some recent publications.

Studies on compactization and decompactization of the genome are of great importance for elucidation of structural mechanisms taking part in the regulation of gene activity. Kinetoplast DNA (kpDNA) is a convenient model for studies of compactization processes. KpDNA represents unique structure ("network"), consisting of catenated circular molecules of two types: minicircles (900 b.p.) and maxicircles (40 000 b.p.). The compactization process of kpDNA in vitro caused by interaction with synthetic peptide-dansylhydraside trivaline was studied. It was shown that at the initial stages the hairpins are observed on minicircles as if triple rings are being organized. The formation of hairpin is probably favoured by the presence in the minicircles of bent DNA, a specific nucleotide sequence causing rigid bending of the DNA helix. The hairpin does not make contact with the neighbouring DNA segment to form a triple ring, because the sizes of minicircles are too small. The minicircles compactization is finished with a complete collapse of the minicircles with the formation of rod-like structures. The catenation causes branching of rod-like structures. As a result of their intermolecular interaction, the branched rod-like structures become thicker. The process is completed with formation of the compact network, its diameter being 3-6 times smaller compared to the initial one.